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What is GENESIS?


Functions of GENESIS

The GENESIS program package is composed of two MD programs (ATDYN, SPDYN) and trajectory analysis tools.

  • CHARMM force field, AMBER force field, MARTINI model, and Go models (Cα Go, all-atom Go, and KB Go)
  • Energy minimization and molecular dynamics simulations
  • Leapfrog, velocity Verlet, and RESPA integrators
  • SHAKE/RATTLE, SETTLE, and LINCS algorithms for bond constraint
  • Bussi, Langevin, and Berendsen thermostat/barostat in the NVT, NPT, NPAT, and NPγT ensembles
  • Replica-exchange molecular dynamics method (REMD) in temperature, pressure, and surface-tension space
  • Generalized replica-exchange with solute tempering (gREST)
  • Replica-exchange umbrella sampling (REUS) with collective variables
  • Multi-dimensional REMD method (T-REMD/P-REMD, T-REMD/REUS, gREST/REUS, etc)
  • Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
  • String method for reaction pathway search
  • Hybrid QM/MM (quantum mechanics/molecular mechanics) calculation
  • Implicit solvent model (Generalized Born/Solvent Accessible Surface Area model)
  • Cryo-EM flexible fitting using all-atom, CG, and implicit solvent models with MD, REMD, and REUS
  • Free-energy perturbation method (FEP)
  • Anharmonic vibrational analysis using SINDO
  • Steered MD and Targeted MD simulations
  • Restrained MD simulations (Distance, angle, dihedral angle, position, etc)
  • Hybrid MPI+OpenMP, hybrid CPU+GPGPU, mixed double+single precision calculations
  • Highly-parallelized Particle mesh Ewald method (PME)
  • Scalable MD simulations for huge systems (> 100,000,000 atoms)
  • Trajectory analysis tools (RMSD, RMSF, PCA, WHAM, MBAR, etc.)
  • Spatial decomposition analysis (SPANA)

MD trajectories obtained by GENESIS can be visualized with VMD and other software. CHARMM-GUI input generator can be used for the preparation of GENESIS input files.


How to cite GENESIS

Any published work which uses GENESIS 1.0 or before might include the reference:
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mol. Sci., 5, 310-323 (2015). 

Any published work which uses GENESIS 1.1.x or 1.2.x should cite the following reference:
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita, J. Compute. Chem. 38, 2193-2206 (2017) (DOI: 10.1002/jcc.24874).